With all the talk about this song I remembered this interview of Bobby and Phil by Marty Martinez & David Gans from 1995 for the Hundred Year Hall: http://www.levity.com/gans/hyh.html
Here's the relevant section:
"MM: Included on this disc is a wonderful song, one of my favorites, "Comes a Time." I've always wondered why it kind of faded from the songbook. And it's great to have it on this CD.
Lesh: Oh, I love the song, too...
Weir: I do, too.
Lesh: ...I think it's a marvelous song.
MM: Why did it fade from the songbook over the years?
Weir: Jerry was always trying to bring it back, but it's one of those songs where there're a couple more chord changes than you can easily remember. So you have to roll over it. And, and we never got around to, uh,you know, we'd - "we gotta work that one up!" "Yeah, next sound check, man!" And...
Weir: ...it never happened.
Lesh: Exactly. The other thing about that song is the introduction was real tricky.
Lesh: Jerry and I would start in what they call "contrary motion" - lines that went in different directions. And it was just the two of us. And then, about three notes later, the other band members would come in. Or did you play in unison with him?
Lesh: Oh, that's right, that' s right - we had a three-part linear, but it was like counterpoint, everybody had to play the right note at the right point. And, uh -
Weir: None of us could remember it.
Lesh: It got pretty tricky there, because I thought I knew where *I* was supposed to start, but it didn't sound right...
Lesh: ...for one thing.
DG: Well, it finally got recorded quite beautifully - in this very room, actually [Bob Weir's home studio] - on Jerry's Reflections album. Then it came back into the Grateful Dead repertoire just a couple years ago - to the delight of the audience, as far as I can tell.
Lesh: Oh, yeah, it's a marvelous song.
Weir: We never did it quite enough to get it as strong as we wanted to do it...
Weir: ...uh, to sort of put it in the "featured ballad," uh, position.
Lesh: Yeah, it had an ending that we could go *out* on, kinda like "Morning Dew"...
Weir: Mm-hmm, mm-hmm.
Lesh: ... or "Stella Blue" or something like that, but we just never did it enough; it's one of those lost opportunities."